Re: [R] caculate the frequencies of the Amino Acids
I sent a private reply to the poster yesterday with the solution to his
problem,
bit evidently he hasn't seen it, so ...
# Function to tabulate an amino acid sequence
# using strsplit and table:
AAtab2 - function(x) {
# Creates a frequency table of the characters in a string
AA - LETTERS[-c(2, 10, 15, 21, 24, 26)]
n - nchar(x)
s - substring(x, 1:n, 1:n)
table(factor(s, levels = AA))
}
AAtabMatrix - function(x) {
# Input x is an amino acid sequence as a character string
if(!is.character(x)) stop('Input must be a character string or vector.')
do.call(rbind, lapply(as.list(x), AAtab2))
}
cheseq - scan(url('http://n4.nabble.com/file/n997581/sequence.txt'), what =
'')
AAtabMatrix(cheseq)
A C D E F G H I K L M N P Q R S T V W Y
[1,] 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[2,] 21 0 25 28 27 24 0 34 39 31 11 20 16 10 17 25 22 33 3 15
[3,] 34 5 15 25 6 35 7 24 23 32 9 12 15 10 17 14 13 36 2 13
[4,] 33 5 17 24 7 36 7 24 24 32 9 13 14 9 17 12 14 36 2 12
[5,] 33 5 16 25 5 35 6 24 23 33 8 12 15 9 17 17 12 35 2 15
[6,] 33 4 15 6 21 30 3 19 23 22 8 8 8 14 17 14 12 24 5 12
[7,] 30 3 13 4 16 22 2 17 16 17 6 6 7 11 15 11 12 18 3 11
[8,] 39 5 21 8 22 39 2 23 29 25 10 8 7 13 22 14 21 25 7 16
[9,] 34 4 17 6 19 30 2 20 24 21 8 7 7 12 17 14 16 21 5 14
[10,] 35 4 17 6 18 31 3 20 23 21 8 7 7 12 18 12 17 21 5 13
Each row represents the frequency table of an individual AA sequence.
DM
On Sat, Jan 2, 2010 at 9:28 PM, che fadialn...@live.com wrote:
Thanks very much the code is working perfectly, but I hope guys that you
can
help me to do the same thing but by using the loop structure, i want to
know
if i am doing right, i want to use the loop structure to scan each sequence
from the file sequence.txt (the file is attached) to get the frequency for
each Amino Acid, and i wrote the following code so far, and i stopped, got
confused, specially that i am a very beginner in R
http://n4.nabble.com/file/n997581/sequence.txt sequence.txt :
x-read.table(sequence.txt,header=FALSE)
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
test-nchar(as.character(x$V1[i]))
frequency-function(X)
{
y-rep(0,20)
for(j in 1:test){
for(i in 1:nrow(x)){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
So how to fix this code, how to give the life for the i and the j in
order to initiate the indexing. Sorry for bothering you guys.
che wrote:
may some one please help me to sort this out, i am trying to writ a R
code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text file,
i
used the following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the i, which suppose to read the
nine rows of the file sequence.txt. the sequence.txt file is attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
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http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997581.html
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[[alternative HTML version deleted]]
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Re: [R] caculate the frequencies of the Amino Acids
Hi fadialnaji,
Take a look at the Biostring package in Bioconductor [1] It might be an
alternative to do what you want.
HTH,
Jorge
[1] http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html
On Fri, Jan 1, 2010 at 11:59 PM, che wrote:
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different
sequences,
i want the code to read the sequence from external text file, i used the
following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the i, which suppose to read the
nine
rows of the file sequence.txt. the sequence.txt file is attached to this
message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
Thanks very much the code is working perfectly, but I hope guys that you can
help me to do the same thing but by using the loop structure, i want to know
if i am doing right, i want to use the loop structure to scan each sequence
from the file sequence.txt (the file is attached) to get the frequency for
each Amino Acid, and i wrote the following code so far, and i stopped, got
confused, specially that i am a very beginner in R
http://n4.nabble.com/file/n997581/sequence.txt sequence.txt :
x-read.table(sequence.txt,header=FALSE)
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
test-nchar(as.character(x$V1[i]))
frequency-function(X)
{
y-rep(0,20)
for(j in 1:test){
for(i in 1:nrow(x)){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
So how to fix this code, how to give the life for the “i” and the “j” in
order to initiate the indexing. Sorry for bothering you guys.
che wrote:
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text file, i
used the following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the i, which suppose to read the
nine rows of the file sequence.txt. the sequence.txt file is attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997581.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
On Jan 3, 2010, at 12:28 AM, che wrote:
Thanks very much the code is working perfectly, but I hope guys that
you can
help me to do the same thing but by using the loop structure, i want
to know
if i am doing right, i want to use the loop structure to scan each
sequence
from the file sequence.txt (the file is attached) to get the
frequency for
each Amino Acid, and i wrote the following code so far, and i
stopped, got
confused, specially that i am a very beginner in R
http://n4.nabble.com/file/n997581/sequence.txt sequence.txt :
x-read.table(sequence.txt,header=FALSE)
AA-
c
('A
','C
','D
','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
test-nchar(as.character(x$V1[i]))
frequency-function(X)
{
y-rep(0,20)
I earlier pointed out that such a structure would be inadequate to
hold the tabulation of more than one sequence. You probably need a
matrix of width = 20 and depth = the number of your sequences.
for(j in 1:test){
for(i in 1:nrow(x)){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
... and here you will need to index y[ , ] with both the proper row
and column.
}
}
return(y)
}
So how to fix this code, how to give the life for the “i” and the
“j” in
order to initiate the indexing. Sorry for bothering you guys.
--
David.
che wrote:
may some one please help me to sort this out, i am trying to writ a
R code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text
file, i
used the following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-
c
('A
','C
','D
','E
','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence,
i dont
know why the loop is not working for the i, which suppose to read
the
nine rows of the file sequence.txt. the sequence.txt file is
attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997581.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] caculate the frequencies of the Amino Acids
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different sequences,
i want the code to read the sequence from external text file, i used the
following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the i, which suppose to read the nine
rows of the file sequence.txt. the sequence.txt file is attached to this
message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997072.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
On Jan 1, 2010, at 11:59 PM, che wrote:
may some one please help me to sort this out, i am trying to writ a
R code
for calculating the frequencies of the amino acids in 9 different
sequences,
i want the code to read the sequence from external text file, i used
the
following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-
c
('A
','C
','D
','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
# at this point you are referencing i but it is not yet being
iterated and might not even exist.
# did you mean j?
# also might be safer to use seq_along()
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
# Is that really working for even one sequence? Without an x
sequence I cannot test, but it looks wrong.
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i
dont
know why the loop is not working for the i, which suppose to read
the nine
rows of the file sequence.txt. the sequence.txt file is attached to
this
message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997072.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
On Jan 2, 2010, at 12:26 AM, David Winsemius wrote:
On Jan 1, 2010, at 11:59 PM, che wrote:
may some one please help me to sort this out, i am trying to writ a
R code
for calculating the frequencies of the amino acids in 9 different
sequences,
i want the code to read the sequence from external text file, i
used the
following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-
c
('A
','C
','D
','E
','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
Further thoughts: If I understand how you are doing this, that
structure would only be large enough for one string's results.
(Seems like this process would be easier if you used table() instead
of for-loops.)
for(j in 1:nchar(as.character(x$V1[i]))){
# at this point you are referencing i but it is not yet being
iterated and might not even exist.
# did you mean j?
# also might be safer to use seq_along()
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
# Is that really working for even one sequence? Without an x
sequence I cannot test, but it looks wrong.
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence,
i dont
know why the loop is not working for the i, which suppose to read
the nine
rows of the file sequence.txt. the sequence.txt file is attached to
this
message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997072.html
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
i know it would be better to ask R to make the data, but i need to sequence
this particular file, because it is data for some Amino Acids and i cant
play with, so i need to ask R to go through the sequence one by one, and
then give me the numbers of each letters of each sequence, i am quite
confused between using i and j and how to iterate both of them and make
them work functionally. i attached the sequence.txt with my original
message, and i will attach it here in case. thanks for your help.
http://n4.nabble.com/file/n997087/sequence.txt sequence.txt
che wrote:
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text file, i
used the following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the i, which suppose to read the
nine rows of the file sequence.txt. the sequence.txt file is attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
--
View this message in context:
http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997087.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] caculate the frequencies of the Amino Acids
On Jan 2, 2010, at 12:55 AM, che wrote:
i know it would be better to ask R to make the data, but i need to
sequence
this particular file, because it is data for some Amino Acids and i
cant
play with, so i need to ask R to go through the sequence one by one,
and
then give me the numbers of each letters of each sequence, i am quite
confused between using i and j and how to iterate both of them
and make
them work functionally. i attached the sequence.txt with my original
message, and i will attach it here in case. thanks for your help.
http://n4.nabble.com/file/n997087/sequence.txt sequence.txt
Sorry. I did not read to the very end. My apologies, hopefully the
following
oneliner will make up for my dereliction of attention.
che wrote:
may some one please help me to sort this out, i am trying to writ a
R code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text
file, i
used the following code to do so:
x-read.table(sequence.txt,header=FALSE)
then i defined an array for 20 amino acids as following:
AA-
c
('A
','C
','D
','E
','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
After copy-pasting the sequences from a browser window to a character
object, seqnc, I then processed it:
seqlines - readLines(textConnection(seqnc))
# Then for the first sequence:
table(strsplit(seqlines[1], vector()) )
A D E F G I K L M N P Q R S T V W Y
21 25 28 27 24 34 39 31 11 20 16 10 17 25 22 33 3 15
# For mass production: The names that resulted from my first effort
were a bit
unwieldly ( 200 characters long) so I unnamed it:
unname( sapply(seqlines, function(x) table(strsplit(x, vector() ) ) ) )
[[1]]
A D E F G I K L M N P Q R S T V W Y
21 25 28 27 24 34 39 31 11 20 16 10 17 25 22 33 3 15
[[2]]
A C D E F G H I K L M N P Q R S T V W Y
34 5 15 25 6 35 7 24 23 32 9 12 15 10 17 14 13 36 2 13
[[3]]
A C D E F G H I K L M N P Q R S T V W Y
33 5 17 24 7 36 7 24 24 32 9 13 14 9 17 12 14 36 2 12
[[4]]
A C D E F G H I K L M N P Q R S T V W Y
33 5 16 25 5 35 6 24 23 33 8 12 15 9 17 17 12 35 2 15
[[5]]
A C D E F G H I K L M N P Q R S T V W Y
33 4 15 6 21 30 3 19 23 22 8 8 8 14 17 14 12 24 5 12
[[6]]
A C D E F G H I K L M N P Q R S T V W Y
30 3 13 4 16 22 2 17 16 17 6 6 7 11 15 11 12 18 3 11
[[7]]
A C D E F G H I K L M N P Q R S T V W Y
39 5 21 8 22 39 2 23 29 25 10 8 7 13 22 14 21 25 7 16
[[8]]
A C D E F G H I K L M N P Q R S T V W Y
34 4 17 6 19 30 2 20 24 21 8 7 7 12 17 14 16 21 5 14
[[9]]
A C D E F G H I K L M N P Q R S T V W Y
35 4 17 6 18 31 3 20 23 21 8 7 7 12 18 12 17 21 5 13
[[10]]
A
5
--
David.
frequency-function(X)
{
y-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence,
i dont
know why the loop is not working for the i, which suppose to read
the
nine rows of the file sequence.txt. the sequence.txt file is
attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
